Package chemaxon.descriptors.scalars
Class LDParameters
java.lang.Object
chemaxon.descriptors.MDParameters
chemaxon.descriptors.SDParameters
chemaxon.descriptors.scalars.LDParameters
Manages parameters for the
LogD
scalar descriptor class.
The native format of the parameter configuration is XML.- Since:
- JChem 2.2
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Field Summary
Modifier and TypeFieldDescriptionstatic final int
default values for parametersstatic final int
static final int
static final int
Fields inherited from class chemaxon.descriptors.MDParameters
asymmetryFactors, cellSize, cellwiseWeights, configFilePath, currentMetricIndex, data, decForm, DEFAULT_ASYMMETRY_FACTOR, DEFAULT_OUTPUT_PRECISION, DEFAULT_SCALE_FACTOR, DEFAULT_WEIGHT, defaultWeight, document, generator, internalSize, length, md, metricIndexes, normalized, outputPrecision, parametrizedMetricNodes, parametrizedMetrics, parametrizedMetricsNode, scaleFactors, screeningConfigurationNode, similarityNode, standardizer, standardizerConfigurationNode, thresholds, tverskyA, tverskyB, weights
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Constructor Summary
ConstructorDescriptionCreates an empty object.LDParameters
(File configFile) Creates a new object based on a given configuration file.LDParameters
(String XMLconfig) Creates a new object based on a given configuration string. -
Method Summary
Modifier and TypeMethodDescriptionprotected float
protected void
Initializes those data members that depend on the XML configuration but are not directly taken from it.protected void
readValues
(boolean all) Picks parameters values from the DOM tree.toString()
Returns the XML configuration in a string.Methods inherited from class chemaxon.descriptors.SDParameters
fromFile, fromString, getNumberOfMetrics, getType, init, processDocument, setLength
Methods inherited from class chemaxon.descriptors.MDParameters
addParameters, addParameters, addParametrizedMetric, addParametrizedMetricNode, addParametrizedMetricsNode, appendParametrizedMetric, checkDocumentVersion, getAsymmetryFactor, getCellSize, getCurrentMetricIndex, getData, getDecForm, getDefaultDocumentFrame, getDefaultStandardizerConfiguration, getDescriptorTypeName, getInternalMetricIndex, getInternalSize, getLength, getMetricIndex, getMetricName, getMetricName, getNumberOfWeights, getNumberOfWeights, getScaleFactor, getScalingHypothesis, getScreeningConfigurationString, getThreshold, getThreshold, getTverskyAlpha, getTverskyBeta, getWeights, importNodes, isAsymmetric, isCellwiseWeights, isNormalized, isScaled, isStandardizationMandatory, isWeighted, readFromXmlFile, readFromXmlString, readMetricParameters, readMetricWeights, setAsymmetryFactor, setCellSize, setCellwiseWeights, setCreateStatistics, setCurrentParametrizedMetric, setNormalized, setOutputPrecision, setParameters, setParameters, setScaleFactor, setScalingHypothesis, setThreshold, setWeights, standardize, toString, writeMetricParameter
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Field Details
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DEFAULT_LOWER_BOUND
public static final int DEFAULT_LOWER_BOUNDdefault values for parameters- See Also:
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DEFAULT_UPPER_BOUND
public static final int DEFAULT_UPPER_BOUND- See Also:
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DEFAULT_STEP_SIZE
public static final int DEFAULT_STEP_SIZE- See Also:
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DEFAULT_PH
public static final int DEFAULT_PH- See Also:
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Constructor Details
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LDParameters
public LDParameters()Creates an empty object. Initializes parameters to default values. -
LDParameters
Creates a new object based on a given configuration file.- Parameters:
configFile
- XML configuration file- Throws:
MDParametersException
- missing or bad XML configuration
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LDParameters
Creates a new object based on a given configuration string.- Parameters:
XMLconfig
- XML configuration string- Throws:
MDParametersException
- missing or bad XML configuration
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Method Details
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toString
Returns the XML configuration in a string.- Overrides:
toString
in classMDParameters
- Returns:
- configuration string in XML format
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initParameters
protected void initParameters()Description copied from class:SDParameters
Initializes those data members that depend on the XML configuration but are not directly taken from it.- Overrides:
initParameters
in classSDParameters
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generate
- Throws:
MDGeneratorException
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readValues
Picks parameters values from the DOM tree.- Overrides:
readValues
in classSDParameters
- Parameters:
all
- indicates if the entire document has to be processed in which case the existing configuration is overwritten- Throws:
MDParametersException
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